Contacts of the helix formed by residues 794 - 804 (chain A) in PDB entry 3L6X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 794 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A VAL* 4.6 0.7 - - - -
791A ARG 3.5 12.3 + - - -
792A GLU* 3.3 13.7 + - - +
793A THR* 1.3 80.8 - - - +
795A GLY* 1.3 58.5 + - - +
796A ILE* 3.4 0.9 - - - +
797A GLU* 2.5 68.1 - - + +
798A LYS* 3.7 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A VAL* 3.7 21.8 - - - -
753A LEU* 5.1 1.5 - - - +
790A LEU* 3.3 20.9 + - - +
793A THR 3.1 3.8 - - - -
794A GLN* 1.3 75.6 - - - +
796A ILE* 1.3 60.7 + - - +
797A GLU 3.3 0.7 - - - -
798A LYS* 3.4 6.2 + - - +
799A LEU* 3.0 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790A LEU* 4.5 2.2 + - + -
791A ARG* 3.9 41.7 - - + +
794A GLN 3.4 0.4 - - - -
795A GLY* 1.3 74.6 - - - +
797A GLU* 1.3 69.5 + - - +
799A LEU* 3.3 5.3 + - - +
800A VAL* 3.0 39.1 + - + +
820A LEU* 4.7 8.1 - - + -
823A ILE* 3.5 39.7 - - + -
829A LEU* 4.5 4.3 - - + -
833A LEU* 3.7 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A GLY 5.6 3.6 - - - +
794A GLN* 2.5 64.1 - - + +
795A GLY 3.3 0.2 - - - -
796A ILE* 1.3 81.7 + - - +
798A LYS* 1.3 59.4 + - + +
800A VAL* 3.7 5.5 - - - +
801A LEU* 2.8 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SO4 3.1 36.8 + - - -
750A VAL* 2.9 33.0 + - + +
751A LYS 3.7 3.4 + - - -
753A LEU* 2.9 34.2 + - + +
754A PRO 3.4 22.7 - - - +
755A GLY* 3.9 10.1 - - - +
756A GLY* 3.8 16.0 - - - +
793A THR 5.4 0.9 - - - -
794A GLN* 3.7 13.9 + - - +
795A GLY* 3.4 8.4 + - - +
796A ILE 3.2 0.6 - - - -
797A GLU* 1.3 74.8 - - + +
799A LEU* 1.3 67.3 + - - +
801A LEU* 3.2 5.5 + - - +
802A ILE* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A LEU* 4.4 9.6 - - + -
773A LEU* 3.3 32.3 - - + -
776A ILE* 5.3 3.8 - - + -
790A LEU* 4.1 9.2 - - + -
795A GLY 3.0 19.7 + - - +
796A ILE* 3.8 6.1 - - - +
798A LYS* 1.3 76.0 - - - +
800A VAL* 1.3 57.8 + - - +
802A ILE* 3.3 2.9 + - - -
803A ASN* 2.8 30.5 + - - +
816A ALA* 3.7 8.6 - - + +
819A VAL* 3.6 25.8 - - + -
820A LEU* 4.0 18.4 - - + -
823A ILE* 3.5 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 800 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A ILE* 3.0 33.0 + - + +
797A GLU* 3.7 5.2 - - - +
799A LEU* 1.3 73.6 - - - +
801A LEU* 1.3 62.8 + - - +
803A ASN* 4.3 5.6 - - - -
804A LYS* 2.8 42.0 + - + +
820A LEU* 4.4 5.8 - - + -
833A LEU* 5.6 0.9 - - + -
838A TRP* 3.9 35.2 - - + +
843A PHE* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 801 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754A PRO* 4.1 16.4 - - + +
755A GLY* 3.8 11.0 - - - +
762A TRP* 3.4 37.7 - - + -
797A GLU 2.8 18.7 + - - +
798A LYS* 3.2 6.0 + - - +
800A VAL* 1.3 77.2 - - - +
802A ILE* 1.3 76.8 + - + +
804A LYS* 3.7 2.3 - - - -
805A SER* 3.2 21.6 + - - -
808A ARG* 4.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 802 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A LEU* 4.0 29.2 - - + -
754A PRO* 4.0 20.2 - - + +
769A VAL* 4.1 8.1 - - + -
773A LEU* 4.1 12.6 - - + -
798A LYS 2.9 23.9 + - - +
799A LEU* 3.8 3.4 - - - +
801A LEU* 1.3 89.4 - - + +
803A ASN* 1.3 64.2 + - - +
805A SER* 3.0 19.2 + - - -
808A ARG* 4.1 8.0 - - - +
812A GLU* 3.8 35.2 - - + +
813A VAL* 3.8 7.7 - - - +
816A ALA* 3.6 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 803 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A LEU 2.8 18.8 + - - +
800A VAL* 3.9 3.4 - - - +
802A ILE* 1.3 76.1 - - - +
804A LYS* 1.3 73.8 + - - +
805A SER 3.3 2.6 + - - +
813A VAL* 3.2 44.0 - - - +
816A ALA* 4.1 7.4 - - + -
817A ALA* 3.5 14.9 - - - +
820A LEU* 3.8 17.5 - - + -
842A ASP 3.9 4.9 + - - -
843A PHE* 3.5 27.3 - - - +
844A GLN 4.7 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 804 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800A VAL* 2.8 35.4 + - + +
801A LEU* 3.7 4.0 - - - +
803A ASN* 1.3 85.9 - - - +
805A SER* 1.3 64.4 + - - +
806A GLY 3.5 1.9 + - - -
838A TRP* 4.5 15.0 - - + -
842A ASP* 2.8 33.9 + - - +
843A PHE* 4.4 9.2 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il